Table 1. Genes with cis-eQTL detected in the population of 140 natural A. thaliana accessions (SCHMITZ-data) contributing to the accession specific presence or absence of transcripts and earlier reported biological function.

Locus	Gene	SNPa	MAFb	Log odds ratio ± SEc	P-valued	Replicatede	Reference
AT2G21045	HAC1	chr2_9028685	0.14	4.84 ± 0.76	1.75 × 10−10	Yes-GBF	Chao et al. 2014
AT5G59340	WOX2	chr5_23935224	0.43	2.82 ± 0.54	1.83 × 10−7	Yes	Lie et al. 2012
AT1G77235	MIR402	chr1_29007464	0.46	7.07 ± 1.02	5.18 × 10−12	No.e	Kim et al. 2010
AT2G38220	APD3	chr2_16017043	0.29	0.37 ± 0.07	3.64 × 10−7	No.e	Luo et al. 2012
AT1G13430	ATST4C	chr1_4601762	0.51	0.36 ± 0.06	3.87 × 10−10	No	Marsolais et al. 2007
AT1G66600	WRKY63	chr1_24217798	0.06	0.14 ± 0.02	3.22 × 10−10	No	Van Aken et al. 2013
AT2G19500	ATCKX2	chr2_8168512	0.07	0.18 ± 0.03	6.13 × 10−9	No	von Schwartzenberg et al. 2007
AT3G27620	AOX1C	chr3_10230473	0.39	0.4 ± 0.07	6.45 × 10−8	No	Wang et al. 2012
AT3G57270	BG1	chr3_22031771	0.06	0.15 ± 0.02	1.09 × 10−9	No	Zavaliev et al. 2013
AT4G01420	CBL5	chr4_583422	0.12	0.2 ± 0.03	7.48 × 10−12	No	Cheong et al. 2010
AT4G02850	DAAR1	chr4_597373	0.06	0.15 ± 0.02	1.41 × 10−9	No	Strauch et al. 2015
AT4G29340	PRF4	chr4_14639984	0.21	0.36 ± 0.07	2.32 × 10−7	No	Deeks et al. 2005

^aTop SNP in association analysis.

^bMinor allele frequency of the top associated SNP in the SCHMITZ-data.

^cLog odds ratio of the top associated SNP ± SE.

^dNominal P-value for the top associated SNP.

^eCould the original association in the SCHMITZ-data be replicated in the DUBIN-data: Yes-GBF, Replicated at Genome Wide Bonferroni threshold; Yes, replicated at Bonferroni threshold correcting for number of markers in ± 1 Mb window of the peak SNP in Dubin-data; No.e, not expressed in DUBIN-data so could not be tested for replication; No, nonsignificant in replication analysis.